fasttrimmatic

Name	fasttrimmatic JSON
Version	1.0.0 JSON
	download
home_page	https://github.com/bbeckley-hub/fasttrimmatic
Summary	Hybrid fastp + Trimmomatic-like FASTQ quality control and trimming tool
upload_time	2025-08-13 14:37:01
maintainer	None
docs_url	None
author	Beckley Brown
requires_python	>=3.7
license	None
keywords
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # Fasttrimmatic

Hybrid fastp + trimmomatic-like FASTQ quality control and trimming tool.

## Features

- Adapter autodetection and trimming with mismatch tolerance
- Leading and trailing quality trimming
- Sliding window quality trimming
- Self-supervised ML-based adaptive trimming (optional)
- Supports single-end and paired-end reads
- Multithreaded processing with progress reporting
- Filters reads by minimum length after trimming

## Installation

```bash
pip install fasttrimmatic
```

Or to install with ML support:

```bash
pip install fasttrimmatic[ml]
```

## Usage

Single-end example:

```bash
fasttrimmatic -i sample.fastq.gz -o trimmed.fastq.gz --use-ml --max-workers 4 --verbose
```

Paired-end example:

```bash
fasttrimmatic --paired -i1 sample_R1.fastq.gz -i2 sample_R2.fastq.gz -o1 trimmed_R1.fastq.gz -o2 trimmed_R2.fastq.gz --use-ml --max-workers 4 --verbose
```

## Author

Beckley Brown  
GitHub: [bbeckley-hub](https://github.com/bbeckley-hub)  
Email: brownbeckley94@gmail.com

            

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